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9qq8

Crystal structure of the catalytic N-terminal domain of the relaxase of plasmid pLS20 in complex with the core region

Method: X-RAY DIFFRACTION D_max: 70.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qq8
deposition_date	2025-03-31
title	Crystal structure of the catalytic N-terminal domain of the relaxase of plasmid pLS20 in complex with the core region
keywords	Bacterial Conjugation, DNA binding, Antibiotic resistance, Firmicutes, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	19.21 Å
rg_electron	18.34 Å
i0	12642300.00
molecular_weight	24342.0 kDa
excluded_volume	29556 Å³
envelope_volume	36257 Å³
shell_volume	17004 Å³
envelope_diameter	73.9 Å
shell_rg	24.30 Å
envelope_rg	18.87 Å
shape_rg	18.33 Å
total_rg	19.23 Å
total_atoms	1698
n_residues	191
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	70.7 Å
rg_real	19.23 Å
rg_real_error	0.57 Å
i0_real	1.2640e+07
i0_real_error	1.7440e+05
rg_reciprocal	19.23 Å
i0_reciprocal	12640000.0000
total_estimate	0.7372
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	22.6 Å
skewness	0.462
kurtosis	0.091
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	1918000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.566; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Relaxase
formula_weight	26963.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1711

GPMDSPGVVLVSKYVSGKSTKFSKYVNYINRDEAVRTEKFQTYNVNKLDGYNQYMGNPEKSSGIFTQHKDSLSPVEKNQLKEIFRQAQKNDSVMWQDVISFDNKWLEERGIYNSQTGWVNEGAIQNSIRKGMEVLLREEQLEQSGVWSAAIHYNTDNIHVHIALVEPNPTKEYGVFTNKKTGEVYQARRGNRKLKTLDKMKSKVANTLMDRDKELSKISQLIHDRIAPKGLKFQ

Source

organism	Bacillus subtilis subsp. natto
ncbi_taxonomy_id	86029
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	;DNA (5'-D(APGPTPTPTPCPCPCPCPTPTPAPTPGPCPTPCPTPT)-3') ;
formula_weight	5712.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

AGTTTCCCCTTATGCTCTT

Entity 3 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	nat
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	13

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6. Citations (1)

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length_a	78.680 Å
length_b	78.680 Å
length_c	158.560 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63 2 2
int_tables_number	182
crystal_system	hexagonal

resolution	2.290 Å
resolution_low	41.760 Å
r_factor	0.2131
r_work	0.2117
r_free	0.2394

fit	/app/data/saxs_computation/qq/9qq8/9qq8.fit
pddf	/app/data/pr_computation/qq/9qq8/9qq8.pr.out
profile	/app/data/saxs_computation/qq/9qq8/9qq8.dat

Crystal structure of the catalytic N-terminal domain of the relaxase of plasmid pLS20 in complex with the core region

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)